Starting phenix.real_space_refine
on Thu Jun  5 15:03:50 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7w6k_32328/06_2025/7w6k_32328.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w6k_32328/06_2025/7w6k_32328.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w6k_32328/06_2025/7w6k_32328.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w6k_32328/06_2025/7w6k_32328.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w6k_32328/06_2025/7w6k_32328.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w6k_32328/06_2025/7w6k_32328.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    4202      2.51       5
     N    1094      2.21       5
     O    1142      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6468
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3234
          Classifications: {'peptide': 410}
          Link IDs: {'PTRANS': 14, 'TRANS': 395}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.19, per 1000 atoms: 0.80
  Number of scatterers: 6468
  At special positions: 0
  Unit cell: (74.88, 92.56, 107.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1142      8.00
     N    1094      7.00
     C    4202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.66
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      82.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 54
      removed outlier: 4.668A  pdb=" N   ASN A  41 " --> pdb=" O   MET A  37 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TRP A  44 " --> pdb=" O   PRO A  40 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLN A  45 " --> pdb=" O   ASN A  41 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A  50 " --> pdb=" O   THR A  46 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 73
    Processing helix  chain 'A' and resid 73 through 78
      removed outlier: 3.578A  pdb=" N   LEU A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 73 through 78'
    Processing helix  chain 'A' and resid 80 through 86
      removed outlier: 4.036A  pdb=" N   ILE A  84 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   GLY A  85 " --> pdb=" O   LYS A  82 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   GLN A  86 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 99
      removed outlier: 4.137A  pdb=" N   ALA A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 131
      removed outlier: 4.097A  pdb=" N   GLY A 110 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 160
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 4.614A  pdb=" N   LYS A 165 " --> pdb=" O   PRO A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 188
      removed outlier: 3.632A  pdb=" N   PHE A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   TYR A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ARG A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 188 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 215
      removed outlier: 3.864A  pdb=" N   LYS A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   TYR A 200 " --> pdb=" O   HIS A 196 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   THR A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 249
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 263 through 288
      removed outlier: 4.775A  pdb=" N   ALA A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   VAL A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   LYS A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   SER A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ILE A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 325
    Processing helix  chain 'A' and resid 332 through 338
      removed outlier: 3.911A  pdb=" N   MET A 338 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 363
      removed outlier: 3.776A  pdb=" N   ILE A 344 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 389
    Processing helix  chain 'A' and resid 459 through 468
      removed outlier: 3.812A  pdb=" N   ILE A 463 " --> pdb=" O   GLN A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 504
      removed outlier: 4.012A  pdb=" N   ASP A 491 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 54
      removed outlier: 4.668A  pdb=" N   ASN B  41 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TRP B  44 " --> pdb=" O   PRO B  40 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLN B  45 " --> pdb=" O   ASN B  41 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL B  50 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 73
    Processing helix  chain 'B' and resid 73 through 78
      removed outlier: 3.578A  pdb=" N   LEU B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU B  78 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 73 through 78'
    Processing helix  chain 'B' and resid 80 through 86
      removed outlier: 4.037A  pdb=" N   ILE B  84 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   GLY B  85 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   GLN B  86 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 99
      removed outlier: 4.137A  pdb=" N   ALA B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 131
      removed outlier: 4.096A  pdb=" N   GLY B 110 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 160
    Processing helix  chain 'B' and resid 160 through 165
      removed outlier: 4.614A  pdb=" N   LYS B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 188
      removed outlier: 3.632A  pdb=" N   PHE B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   TYR B 186 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ARG B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B 188 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 215
      removed outlier: 3.864A  pdb=" N   LYS B 193 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   TYR B 200 " --> pdb=" O   HIS B 196 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   THR B 201 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 249
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 263 through 288
      removed outlier: 4.775A  pdb=" N   ALA B 271 " --> pdb=" O   LYS B 267 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   VAL B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   LYS B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ILE B 278 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 325
    Processing helix  chain 'B' and resid 332 through 338
      removed outlier: 3.910A  pdb=" N   MET B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 363
      removed outlier: 3.776A  pdb=" N   ILE B 344 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG B 345 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 389
    Processing helix  chain 'B' and resid 459 through 468
      removed outlier: 3.812A  pdb=" N   ILE B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 504
      removed outlier: 4.012A  pdb=" N   ASP B 491 " --> pdb=" O   VAL B 487 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU B 492 " --> pdb=" O   ALA B 488 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1386 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 1.96 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1300
        1.33 -     1.45: 1511
        1.45 -     1.57: 3755
        1.57 -     1.69: 0
        1.69 -     1.82: 42
  Bond restraints: 6608
  Sorted by residual:
  bond pdb=" CA  SER B 358 "
       pdb=" CB  SER B 358 "
    ideal  model  delta    sigma   weight residual
    1.528  1.466  0.063 1.56e-02 4.11e+03 1.62e+01
  bond pdb=" CA  SER A 358 "
       pdb=" CB  SER A 358 "
    ideal  model  delta    sigma   weight residual
    1.528  1.466  0.063 1.56e-02 4.11e+03 1.61e+01
  bond pdb=" CA  SER B 360 "
       pdb=" CB  SER B 360 "
    ideal  model  delta    sigma   weight residual
    1.529  1.470  0.059 1.58e-02 4.01e+03 1.40e+01
  bond pdb=" N   PRO A 369 "
       pdb=" CD  PRO A 369 "
    ideal  model  delta    sigma   weight residual
    1.473  1.525 -0.052 1.40e-02 5.10e+03 1.39e+01
  bond pdb=" N   PRO B 369 "
       pdb=" CD  PRO B 369 "
    ideal  model  delta    sigma   weight residual
    1.473  1.525 -0.052 1.40e-02 5.10e+03 1.39e+01
  ... (remaining 6603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 8196
        1.85 -     3.70: 581
        3.70 -     5.54: 143
        5.54 -     7.39: 32
        7.39 -     9.24: 10
  Bond angle restraints: 8962
  Sorted by residual:
  angle pdb=" N   ILE B 252 "
        pdb=" CA  ILE B 252 "
        pdb=" C   ILE B 252 "
      ideal   model   delta    sigma   weight residual
     108.35   99.46    8.89 1.32e+00 5.74e-01 4.54e+01
  angle pdb=" N   ILE A 252 "
        pdb=" CA  ILE A 252 "
        pdb=" C   ILE A 252 "
      ideal   model   delta    sigma   weight residual
     108.35   99.46    8.89 1.32e+00 5.74e-01 4.53e+01
  angle pdb=" N   PHE B 470 "
        pdb=" CA  PHE B 470 "
        pdb=" C   PHE B 470 "
      ideal   model   delta    sigma   weight residual
     110.23  100.99    9.24 1.45e+00 4.76e-01 4.06e+01
  angle pdb=" N   PHE A 470 "
        pdb=" CA  PHE A 470 "
        pdb=" C   PHE A 470 "
      ideal   model   delta    sigma   weight residual
     110.23  100.99    9.24 1.45e+00 4.76e-01 4.06e+01
  angle pdb=" N   GLY A 114 "
        pdb=" CA  GLY A 114 "
        pdb=" C   GLY A 114 "
      ideal   model   delta    sigma   weight residual
     112.50  119.17   -6.67 1.16e+00 7.43e-01 3.30e+01
  ... (remaining 8957 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 3484
       17.73 -    35.45: 374
       35.45 -    53.18: 68
       53.18 -    70.90: 6
       70.90 -    88.63: 4
  Dihedral angle restraints: 3936
    sinusoidal: 1542
      harmonic: 2394
  Sorted by residual:
  dihedral pdb=" C   PHE B 248 "
           pdb=" N   PHE B 248 "
           pdb=" CA  PHE B 248 "
           pdb=" CB  PHE B 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.88   12.28     0      2.50e+00 1.60e-01 2.41e+01
  dihedral pdb=" C   PHE A 248 "
           pdb=" N   PHE A 248 "
           pdb=" CA  PHE A 248 "
           pdb=" CB  PHE A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.86   12.26     0      2.50e+00 1.60e-01 2.40e+01
  dihedral pdb=" C   TYR A 257 "
           pdb=" N   TYR A 257 "
           pdb=" CA  TYR A 257 "
           pdb=" CB  TYR A 257 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.00   11.40     0      2.50e+00 1.60e-01 2.08e+01
  ... (remaining 3933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 924
       0.086 -    0.172: 78
       0.172 -    0.259: 30
       0.259 -    0.345: 8
       0.345 -    0.431: 4
  Chirality restraints: 1044
  Sorted by residual:
  chirality pdb=" CA  PHE B 248 "
            pdb=" N   PHE B 248 "
            pdb=" C   PHE B 248 "
            pdb=" CB  PHE B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.64e+00
  chirality pdb=" CA  PHE A 248 "
            pdb=" N   PHE A 248 "
            pdb=" C   PHE A 248 "
            pdb=" CB  PHE A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.64e+00
  chirality pdb=" CA  TYR A 257 "
            pdb=" N   TYR A 257 "
            pdb=" C   TYR A 257 "
            pdb=" CB  TYR A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.04e+00
  ... (remaining 1041 not shown)

  Planarity restraints: 1112
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 161 "    0.020 2.00e-02 2.50e+03   4.07e-02 1.65e+01
        pdb=" C   PRO A 161 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PRO A 161 "    0.026 2.00e-02 2.50e+03
        pdb=" N   TYR A 162 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 161 "    0.020 2.00e-02 2.50e+03   4.06e-02 1.65e+01
        pdb=" C   PRO B 161 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PRO B 161 "    0.026 2.00e-02 2.50e+03
        pdb=" N   TYR B 162 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 163 "   -0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   ILE B 163 "    0.063 2.00e-02 2.50e+03
        pdb=" O   ILE B 163 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS B 164 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1109 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2519
        2.85 -     3.36: 7355
        3.36 -     3.87: 10787
        3.87 -     4.39: 12544
        4.39 -     4.90: 19461
  Nonbonded interactions: 52666
  Sorted by model distance:
  nonbonded pdb=" N   SER A 221 "
            pdb=" OE2 GLU A 289 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" N   SER B 221 "
            pdb=" OE2 GLU B 289 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" OD1 ASP A 135 "
            pdb=" OG  SER A 138 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" OD1 ASP B 135 "
            pdb=" OG  SER B 138 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" NZ  LYS B 232 "
            pdb=" OD1 ASP B 279 "
     model   vdw
     2.366 3.120
  ... (remaining 52661 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.410
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   6608  Z= 0.485
  Angle     :  1.134   9.238   8962  Z= 0.794
  Chirality :  0.069   0.431   1044
  Planarity :  0.006   0.041   1112
  Dihedral  : 14.610  88.630   2392
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 47.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.06 %
    Favored  : 87.93 %
  Cbeta Deviations :  0.52 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.24), residues: 812
  helix: -1.77 (0.18), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.84 (0.34), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  44 
 HIS   0.010   0.002   HIS A 226 
 PHE   0.040   0.003   PHE A 248 
 TYR   0.020   0.002   TYR A 247 
 ARG   0.005   0.001   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14333 (  466)
  hydrogen bonds       : angle       6.64181 ( 1386)
  covalent geometry    : bond        0.00737 ( 6608)
  covalent geometry    : angle       1.13364 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 175
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.8116 (t80) cc_final: 0.7916 (t80)
REVERT: B   77 LEU cc_start: 0.8760 (pp) cc_final: 0.8544 (tt)
  outliers start: 14
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1910
  time to fit residues: 46.2844
Evaluate side-chains
  110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:   20.0000
   chunk 33 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 132 ASN
A 179 ASN
A 219 ASN
A 330 GLN
A 377 HIS
A 384 ASN
A 390 GLN
B  86 GLN
B 132 ASN
B 219 ASN
B 330 GLN
B 377 HIS
B 390 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.095355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.071947 restraints weight = 19454.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.075084 restraints weight = 10498.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.077236 restraints weight = 7059.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6608  Z= 0.195
  Angle     :  0.818   8.483   8962  Z= 0.414
  Chirality :  0.045   0.218   1044
  Planarity :  0.005   0.055   1112
  Dihedral  :  5.390  21.633    896
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.54 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.27), residues: 812
  helix: -0.51 (0.19), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.54 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  44 
 HIS   0.013   0.002   HIS A 322 
 PHE   0.026   0.002   PHE A 476 
 TYR   0.025   0.002   TYR A 269 
 ARG   0.005   0.001   ARG A 502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05348 (  466)
  hydrogen bonds       : angle       4.93453 ( 1386)
  covalent geometry    : bond        0.00445 ( 6608)
  covalent geometry    : angle       0.81784 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.9178 (t80)
REVERT: A  169 TYR cc_start: 0.7669 (m-80) cc_final: 0.7366 (m-10)
REVERT: A  280 GLU cc_start: 0.9533 (tp30) cc_final: 0.9224 (mt-10)
REVERT: A  375 HIS cc_start: 0.9518 (m90) cc_final: 0.9023 (m90)
REVERT: A  470 PHE cc_start: 0.8545 (m-10) cc_final: 0.8315 (m-80)
REVERT: B  125 PHE cc_start: 0.9517 (OUTLIER) cc_final: 0.9229 (t80)
REVERT: B  279 ASP cc_start: 0.8832 (m-30) cc_final: 0.8381 (t70)
REVERT: B  280 GLU cc_start: 0.9497 (tp30) cc_final: 0.9177 (mt-10)
REVERT: B  375 HIS cc_start: 0.9447 (m90) cc_final: 0.9012 (m90)
REVERT: B  485 GLU cc_start: 0.8833 (tp30) cc_final: 0.8575 (tm-30)
  outliers start: 29
  outliers final: 17
  residues processed: 157
  average time/residue: 0.1375
  time to fit residues: 30.7555
Evaluate side-chains
  119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue  125 PHE
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  505 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0050
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    0.7196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 330 GLN
B 330 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.093826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.070683 restraints weight = 19262.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.073710 restraints weight = 10031.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.075815 restraints weight = 6616.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.4391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6608  Z= 0.156
  Angle     :  0.698   9.830   8962  Z= 0.350
  Chirality :  0.042   0.212   1044
  Planarity :  0.005   0.036   1112
  Dihedral  :  5.074  21.490    896
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 20.40 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.28), residues: 812
  helix:  0.29 (0.19), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.23 (0.48), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  44 
 HIS   0.014   0.002   HIS A 322 
 PHE   0.030   0.002   PHE B 248 
 TYR   0.024   0.002   TYR B 269 
 ARG   0.003   0.000   ARG B 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04588 (  466)
  hydrogen bonds       : angle       4.52137 ( 1386)
  covalent geometry    : bond        0.00344 ( 6608)
  covalent geometry    : angle       0.69826 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 119
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.7339 (mpp) cc_final: 0.7133 (pmm)
REVERT: A  125 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.9216 (t80)
REVERT: A  279 ASP cc_start: 0.8825 (m-30) cc_final: 0.8480 (t70)
REVERT: A  280 GLU cc_start: 0.9491 (tp30) cc_final: 0.9216 (mt-10)
REVERT: A  303 GLN cc_start: 0.8283 (tp40) cc_final: 0.7863 (mm110)
REVERT: A  375 HIS cc_start: 0.9528 (m90) cc_final: 0.9046 (m90)
REVERT: A  381 GLN cc_start: 0.8847 (mt0) cc_final: 0.8496 (mt0)
REVERT: B   45 GLN cc_start: 0.9341 (mm110) cc_final: 0.9111 (mp10)
REVERT: B   77 LEU cc_start: 0.9464 (mm) cc_final: 0.8956 (tt)
REVERT: B  239 SER cc_start: 0.9694 (m) cc_final: 0.9399 (p)
REVERT: B  247 TYR cc_start: 0.8843 (t80) cc_final: 0.7807 (t80)
REVERT: B  248 PHE cc_start: 0.7703 (m-10) cc_final: 0.7135 (m-10)
REVERT: B  258 MET cc_start: 0.7884 (ptt) cc_final: 0.7499 (ttp)
REVERT: B  303 GLN cc_start: 0.8190 (tp40) cc_final: 0.7712 (mm110)
REVERT: B  375 HIS cc_start: 0.9457 (m90) cc_final: 0.8985 (m90)
REVERT: B  470 PHE cc_start: 0.8115 (m-80) cc_final: 0.7759 (m-80)
REVERT: B  486 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8661 (m)
  outliers start: 37
  outliers final: 20
  residues processed: 142
  average time/residue: 0.1375
  time to fit residues: 28.1131
Evaluate side-chains
  116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  262 GLU
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    0.0870
   chunk 25 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    0.3980
   chunk 18 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 330 GLN
** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 384 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.094248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.070995 restraints weight = 18775.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.073976 restraints weight = 9827.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.076118 restraints weight = 6537.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.4916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6608  Z= 0.140
  Angle     :  0.659   8.257   8962  Z= 0.332
  Chirality :  0.040   0.144   1044
  Planarity :  0.004   0.034   1112
  Dihedral  :  4.818  19.254    896
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 22.84 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.29), residues: 812
  helix:  0.66 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.82 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  44 
 HIS   0.009   0.001   HIS B 322 
 PHE   0.036   0.002   PHE A 248 
 TYR   0.027   0.002   TYR B  75 
 ARG   0.005   0.000   ARG B 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (  466)
  hydrogen bonds       : angle       4.34886 ( 1386)
  covalent geometry    : bond        0.00303 ( 6608)
  covalent geometry    : angle       0.65940 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8438 (t)
REVERT: A  125 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.9199 (t80)
REVERT: A  230 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7735 (t)
REVERT: A  243 CYS cc_start: 0.9451 (t) cc_final: 0.9175 (t)
REVERT: A  279 ASP cc_start: 0.8921 (m-30) cc_final: 0.8606 (t70)
REVERT: A  280 GLU cc_start: 0.9491 (tp30) cc_final: 0.9184 (mt-10)
REVERT: A  303 GLN cc_start: 0.8281 (tp40) cc_final: 0.7864 (mm110)
REVERT: A  375 HIS cc_start: 0.9523 (m90) cc_final: 0.9022 (m90)
REVERT: A  459 GLN cc_start: 0.8752 (mt0) cc_final: 0.8364 (pt0)
REVERT: A  470 PHE cc_start: 0.8332 (m-80) cc_final: 0.7806 (m-80)
REVERT: B   45 GLN cc_start: 0.9332 (mm110) cc_final: 0.9054 (mp10)
REVERT: B  102 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8270 (t)
REVERT: B  106 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9026 (m)
REVERT: B  230 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7743 (t)
REVERT: B  247 TYR cc_start: 0.8981 (t80) cc_final: 0.7937 (t80)
REVERT: B  248 PHE cc_start: 0.8016 (m-80) cc_final: 0.7338 (m-10)
REVERT: B  279 ASP cc_start: 0.9084 (m-30) cc_final: 0.8792 (t70)
REVERT: B  375 HIS cc_start: 0.9466 (m90) cc_final: 0.9007 (m90)
REVERT: B  382 ASP cc_start: 0.9186 (t70) cc_final: 0.8947 (p0)
REVERT: B  470 PHE cc_start: 0.8116 (m-80) cc_final: 0.7792 (m-80)
  outliers start: 35
  outliers final: 22
  residues processed: 139
  average time/residue: 0.1358
  time to fit residues: 27.3156
Evaluate side-chains
  127 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 73 optimal weight:    0.6980
   chunk 41 optimal weight:   20.0000
   chunk 27 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 330 GLN
** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.089876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.066748 restraints weight = 19221.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.069517 restraints weight = 10347.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.071564 restraints weight = 6988.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.5197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6608  Z= 0.225
  Angle     :  0.697   9.636   8962  Z= 0.358
  Chirality :  0.043   0.359   1044
  Planarity :  0.005   0.033   1112
  Dihedral  :  4.756  19.428    896
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 24.57 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.30), residues: 812
  helix:  0.74 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.66 (0.51), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 301 
 HIS   0.009   0.001   HIS A 322 
 PHE   0.040   0.002   PHE A 248 
 TYR   0.023   0.002   TYR B  75 
 ARG   0.004   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04415 (  466)
  hydrogen bonds       : angle       4.33645 ( 1386)
  covalent geometry    : bond        0.00491 ( 6608)
  covalent geometry    : angle       0.69651 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 93
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9176 (t80)
REVERT: A  212 MET cc_start: 0.8855 (mmp) cc_final: 0.8622 (mmp)
REVERT: A  223 GLU cc_start: 0.8317 (tt0) cc_final: 0.7148 (tm-30)
REVERT: A  230 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8097 (t)
REVERT: A  243 CYS cc_start: 0.9511 (t) cc_final: 0.9073 (t)
REVERT: A  279 ASP cc_start: 0.8904 (m-30) cc_final: 0.8468 (t70)
REVERT: A  280 GLU cc_start: 0.9483 (tp30) cc_final: 0.9117 (mt-10)
REVERT: A  303 GLN cc_start: 0.8524 (tp40) cc_final: 0.8095 (tp40)
REVERT: A  375 HIS cc_start: 0.9534 (m90) cc_final: 0.9051 (m90)
REVERT: A  382 ASP cc_start: 0.9256 (t70) cc_final: 0.9035 (p0)
REVERT: A  470 PHE cc_start: 0.8224 (m-80) cc_final: 0.7715 (m-80)
REVERT: B  279 ASP cc_start: 0.9091 (m-30) cc_final: 0.8813 (t70)
REVERT: B  375 HIS cc_start: 0.9498 (m90) cc_final: 0.9048 (m90)
REVERT: B  470 PHE cc_start: 0.8331 (m-80) cc_final: 0.7913 (m-80)
  outliers start: 37
  outliers final: 30
  residues processed: 117
  average time/residue: 0.1287
  time to fit residues: 22.1615
Evaluate side-chains
  116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 84
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  461 SER
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  505 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 36 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.091450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.067540 restraints weight = 19106.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.070402 restraints weight = 10331.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.072426 restraints weight = 7034.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.5493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6608  Z= 0.151
  Angle     :  0.668   9.528   8962  Z= 0.333
  Chirality :  0.040   0.175   1044
  Planarity :  0.004   0.033   1112
  Dihedral  :  4.699  21.735    896
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 25.43 %
    Favored  : 69.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.30), residues: 812
  helix:  0.93 (0.20), residues: 642
  sheet:  None (None), residues: 0
  loop : -1.82 (0.50), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  44 
 HIS   0.009   0.001   HIS A 322 
 PHE   0.026   0.002   PHE B 148 
 TYR   0.026   0.002   TYR B  75 
 ARG   0.004   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04199 (  466)
  hydrogen bonds       : angle       4.21412 ( 1386)
  covalent geometry    : bond        0.00335 ( 6608)
  covalent geometry    : angle       0.66750 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 98
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8345 (t)
REVERT: A  125 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9176 (t80)
REVERT: A  196 HIS cc_start: 0.3116 (OUTLIER) cc_final: 0.2908 (t-90)
REVERT: A  223 GLU cc_start: 0.8223 (tt0) cc_final: 0.7033 (tm-30)
REVERT: A  230 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7946 (t)
REVERT: A  243 CYS cc_start: 0.9496 (t) cc_final: 0.9034 (t)
REVERT: A  279 ASP cc_start: 0.8882 (m-30) cc_final: 0.8457 (t70)
REVERT: A  280 GLU cc_start: 0.9475 (tp30) cc_final: 0.9133 (mt-10)
REVERT: A  303 GLN cc_start: 0.8419 (tp40) cc_final: 0.7448 (tp-100)
REVERT: A  375 HIS cc_start: 0.9519 (m90) cc_final: 0.9036 (m90)
REVERT: A  470 PHE cc_start: 0.8104 (m-80) cc_final: 0.7599 (m-80)
REVERT: A  496 GLU cc_start: 0.9263 (tp30) cc_final: 0.8660 (tp30)
REVERT: B  102 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8344 (t)
REVERT: B  106 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9031 (m)
REVERT: B  223 GLU cc_start: 0.8330 (tt0) cc_final: 0.7282 (tm-30)
REVERT: B  230 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7940 (t)
REVERT: B  243 CYS cc_start: 0.9355 (t) cc_final: 0.9040 (t)
REVERT: B  279 ASP cc_start: 0.9076 (m-30) cc_final: 0.8748 (t70)
REVERT: B  375 HIS cc_start: 0.9482 (m90) cc_final: 0.9025 (m90)
REVERT: B  496 GLU cc_start: 0.9186 (tp30) cc_final: 0.8668 (tp30)
  outliers start: 35
  outliers final: 25
  residues processed: 120
  average time/residue: 0.1287
  time to fit residues: 23.0177
Evaluate side-chains
  117 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 85
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0570
   chunk 29 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   chunk 76 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0060
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.3314

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.093592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.070033 restraints weight = 18675.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.073010 restraints weight = 10048.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.075075 restraints weight = 6762.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.5769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6608  Z= 0.127
  Angle     :  0.650  10.000   8962  Z= 0.323
  Chirality :  0.040   0.197   1044
  Planarity :  0.004   0.033   1112
  Dihedral  :  4.619  19.616    896
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 27.01 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.30), residues: 812
  helix:  1.05 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.90 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  44 
 HIS   0.007   0.001   HIS A 322 
 PHE   0.027   0.002   PHE B 148 
 TYR   0.029   0.001   TYR B  75 
 ARG   0.003   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03999 (  466)
  hydrogen bonds       : angle       4.15148 ( 1386)
  covalent geometry    : bond        0.00271 ( 6608)
  covalent geometry    : angle       0.64962 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8438 (t)
REVERT: A  223 GLU cc_start: 0.8103 (tt0) cc_final: 0.7037 (tm-30)
REVERT: A  230 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7772 (t)
REVERT: A  243 CYS cc_start: 0.9471 (t) cc_final: 0.8936 (t)
REVERT: A  248 PHE cc_start: 0.8718 (m-10) cc_final: 0.8198 (m-10)
REVERT: A  279 ASP cc_start: 0.8885 (m-30) cc_final: 0.8488 (t70)
REVERT: A  280 GLU cc_start: 0.9400 (tp30) cc_final: 0.9136 (mt-10)
REVERT: A  303 GLN cc_start: 0.8311 (tp40) cc_final: 0.7303 (tp-100)
REVERT: A  375 HIS cc_start: 0.9505 (m90) cc_final: 0.9029 (m90)
REVERT: A  470 PHE cc_start: 0.8103 (m-80) cc_final: 0.7572 (m-80)
REVERT: A  496 GLU cc_start: 0.9239 (tp30) cc_final: 0.8543 (tp30)
REVERT: B  102 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8417 (t)
REVERT: B  106 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9039 (m)
REVERT: B  230 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7766 (t)
REVERT: B  279 ASP cc_start: 0.9109 (m-30) cc_final: 0.8820 (t70)
REVERT: B  375 HIS cc_start: 0.9473 (m90) cc_final: 0.9021 (m90)
REVERT: B  470 PHE cc_start: 0.8475 (m-80) cc_final: 0.7963 (m-80)
REVERT: B  496 GLU cc_start: 0.9166 (tp30) cc_final: 0.8571 (tp30)
  outliers start: 29
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1306
  time to fit residues: 22.4867
Evaluate side-chains
  111 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 41 optimal weight:   20.0000
   chunk 69 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 13 optimal weight:    8.9990
   overall best weight:    1.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 ASN
** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.091599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.067062 restraints weight = 19413.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.069836 restraints weight = 10846.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.071777 restraints weight = 7542.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.5951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6608  Z= 0.172
  Angle     :  0.686   9.595   8962  Z= 0.343
  Chirality :  0.040   0.179   1044
  Planarity :  0.005   0.035   1112
  Dihedral  :  4.486  19.501    896
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 27.16 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.30), residues: 812
  helix:  1.26 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.88 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 301 
 HIS   0.008   0.001   HIS B 322 
 PHE   0.034   0.002   PHE B 248 
 TYR   0.028   0.002   TYR B  75 
 ARG   0.004   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04095 (  466)
  hydrogen bonds       : angle       4.13024 ( 1386)
  covalent geometry    : bond        0.00386 ( 6608)
  covalent geometry    : angle       0.68622 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.8261 (tt0) cc_final: 0.7085 (tm-30)
REVERT: A  230 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8085 (t)
REVERT: A  243 CYS cc_start: 0.9149 (t) cc_final: 0.8946 (t)
REVERT: A  279 ASP cc_start: 0.8879 (m-30) cc_final: 0.8634 (t70)
REVERT: A  280 GLU cc_start: 0.9439 (tp30) cc_final: 0.9219 (mt-10)
REVERT: A  303 GLN cc_start: 0.8493 (tp40) cc_final: 0.7530 (tp-100)
REVERT: A  375 HIS cc_start: 0.9511 (m90) cc_final: 0.9018 (m90)
REVERT: A  470 PHE cc_start: 0.8092 (m-80) cc_final: 0.7593 (m-80)
REVERT: A  496 GLU cc_start: 0.9290 (tp30) cc_final: 0.8689 (tp30)
REVERT: B  230 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8043 (t)
REVERT: B  274 ASP cc_start: 0.8747 (p0) cc_final: 0.8387 (p0)
REVERT: B  375 HIS cc_start: 0.9484 (m90) cc_final: 0.9003 (m90)
REVERT: B  382 ASP cc_start: 0.9253 (t70) cc_final: 0.9021 (p0)
REVERT: B  470 PHE cc_start: 0.8343 (m-80) cc_final: 0.7746 (m-80)
REVERT: B  496 GLU cc_start: 0.9223 (tp30) cc_final: 0.8714 (tp30)
  outliers start: 30
  outliers final: 26
  residues processed: 106
  average time/residue: 0.1323
  time to fit residues: 20.6274
Evaluate side-chains
  111 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0030
   chunk 55 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0870
   chunk 45 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.4568

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 330 GLN
A 384 ASN
** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.093384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.069839 restraints weight = 19411.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.072769 restraints weight = 10568.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.074786 restraints weight = 7199.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.6133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6608  Z= 0.128
  Angle     :  0.654   8.336   8962  Z= 0.328
  Chirality :  0.040   0.180   1044
  Planarity :  0.004   0.033   1112
  Dihedral  :  4.498  20.245    896
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 27.87 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.30), residues: 812
  helix:  1.26 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.02 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  44 
 HIS   0.012   0.001   HIS B 322 
 PHE   0.023   0.002   PHE B 148 
 TYR   0.030   0.001   TYR B  75 
 ARG   0.003   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  466)
  hydrogen bonds       : angle       4.05236 ( 1386)
  covalent geometry    : bond        0.00272 ( 6608)
  covalent geometry    : angle       0.65383 ( 8962)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8529 (t)
REVERT: A  223 GLU cc_start: 0.8121 (tt0) cc_final: 0.7141 (tm-30)
REVERT: A  230 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7885 (t)
REVERT: A  303 GLN cc_start: 0.8317 (tp40) cc_final: 0.7349 (tp-100)
REVERT: A  375 HIS cc_start: 0.9498 (m90) cc_final: 0.9004 (m90)
REVERT: A  496 GLU cc_start: 0.9301 (tp30) cc_final: 0.8562 (tp30)
REVERT: B  102 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8477 (t)
REVERT: B  106 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.9020 (m)
REVERT: B  230 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7850 (t)
REVERT: B  375 HIS cc_start: 0.9461 (m90) cc_final: 0.8970 (m90)
REVERT: B  470 PHE cc_start: 0.8369 (m-80) cc_final: 0.7732 (m-80)
REVERT: B  496 GLU cc_start: 0.9140 (tp30) cc_final: 0.8541 (tp30)
  outliers start: 25
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1321
  time to fit residues: 20.3036
Evaluate side-chains
  105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0040
   chunk 20 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    0.2980
   overall best weight:    0.7394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 ASN
** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.093304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.069895 restraints weight = 19249.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.072819 restraints weight = 10513.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.074815 restraints weight = 7157.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.6283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6608  Z= 0.130
  Angle     :  0.669   8.914   8962  Z= 0.335
  Chirality :  0.040   0.182   1044
  Planarity :  0.004   0.033   1112
  Dihedral  :  4.438  20.613    896
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 27.73 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.30), residues: 812
  helix:  1.36 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.05 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  44 
 HIS   0.010   0.001   HIS B 322 
 PHE   0.023   0.002   PHE B 148 
 TYR   0.029   0.002   TYR B  75 
 ARG   0.003   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03844 (  466)
  hydrogen bonds       : angle       4.03764 ( 1386)
  covalent geometry    : bond        0.00285 ( 6608)
  covalent geometry    : angle       0.66939 ( 8962)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8539 (t)
REVERT: A  223 GLU cc_start: 0.8053 (tt0) cc_final: 0.7109 (tm-30)
REVERT: A  230 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7850 (t)
REVERT: A  258 MET cc_start: 0.8167 (tmm) cc_final: 0.7965 (tmm)
REVERT: A  303 GLN cc_start: 0.8367 (tp40) cc_final: 0.7622 (tt0)
REVERT: A  375 HIS cc_start: 0.9501 (m90) cc_final: 0.8990 (m90)
REVERT: A  470 PHE cc_start: 0.8375 (m-80) cc_final: 0.8164 (m-80)
REVERT: A  496 GLU cc_start: 0.9274 (tp30) cc_final: 0.8767 (tp30)
REVERT: B  102 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8438 (t)
REVERT: B  106 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.9044 (m)
REVERT: B  230 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7851 (t)
REVERT: B  375 HIS cc_start: 0.9464 (m90) cc_final: 0.8995 (m90)
REVERT: B  381 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9035 (mm110)
REVERT: B  470 PHE cc_start: 0.8328 (m-80) cc_final: 0.7668 (m-80)
REVERT: B  496 GLU cc_start: 0.9143 (tp30) cc_final: 0.8567 (tp30)
  outliers start: 24
  outliers final: 19
  residues processed: 97
  average time/residue: 0.2172
  time to fit residues: 31.3295
Evaluate side-chains
  102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0370
   chunk 70 optimal weight:    0.9980
   chunk 77 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.7458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 ASN
A 390 GLN
** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 390 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.093190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.070052 restraints weight = 19585.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.073008 restraints weight = 10708.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.074721 restraints weight = 7248.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.6391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6608  Z= 0.129
  Angle     :  0.656   8.707   8962  Z= 0.329
  Chirality :  0.039   0.176   1044
  Planarity :  0.004   0.033   1112
  Dihedral  :  4.386  20.313    896
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 27.59 %
    Favored  : 68.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.30), residues: 812
  helix:  1.44 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.05 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  44 
 HIS   0.009   0.001   HIS B 322 
 PHE   0.022   0.002   PHE B 148 
 TYR   0.029   0.001   TYR B  75 
 ARG   0.003   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03798 (  466)
  hydrogen bonds       : angle       4.02071 ( 1386)
  covalent geometry    : bond        0.00281 ( 6608)
  covalent geometry    : angle       0.65608 ( 8962)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2880.91 seconds
wall clock time: 52 minutes 9.02 seconds (3129.02 seconds total)